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Microbial activity has been proposed to play an important role in the genesis of manganese (Mn) carbonate deposition in natural sediments, with microbial reduction of Mn(IV) oxides as a crucial factor that enhances the saturation state of Mn carbonates in pore waters. Recently, the nucleation of Mn carbonates on cellular templates has been suggested to represent a further microbial control. However, microstructural evidence for this model remains tentative and the Mn carbonate nucleation pathway is still unconstrained. Here we report petrographic and in-situ chemistry that supports the direct role(s) of microbes in the formation of Mn carbonates in the giant Malkansu Mn metallogenic belt at West Kunlun, Northwest China. The Mn carbonate ores exhibit negative δ13C values (−10.2 to −12.7‰) that indicate the microbial reduction of Mn oxide. Microscopic data show that the Mn carbonates exhibit spheroidal rod and dumbbell-like shaped morphologies with a well-defined core-shell structure. These carbonates are intimately associated with net-like organic matter. An incubation experiment was also carried out showing that biogenic Mn carbonate minerals share a strikingly similar crystal form with the natural Mn ore samples. Together, these results provide further evidence for a dual role of microbes in Mn‑carbonate ore formation: Mn(II) and carbonate produced by the microbial reduction of Mn(IV) oxides, and the nucleation of Mn carbonate minerals on cellular surfaces and/or organic matrices. Potentially, these Mn carbonates may have self-assembled to form rod- and dumbbell-like shaped morphologies, analogous to other carbonate systems. The unique core-shell structure observed herein also indicates that the formation of Mn‑carbonates mediated by microbes follows a heterogeneous nucleation pathway. [ABSTRACT FROM AUTHOR]